GeneTribe

GeneTribe infers homology among closely related genomes by incorporating gene collinearity to improve accuracy and scalability in polyploid-rich clades such as the Triticeae tribe.

Key Features:

• Collinearity-Incorporating Strategy: Integrates gene collinearity with homology inference to increase accuracy and scalability when comparing closely related genomes.
• Multilevel Homolog-Identification Pipeline: Combines macrocollinearity and microscale collinearity analyses to resolve structural rearrangements and detailed homolog relationships.
• Triticeae-GeneTribe Database: A homology database constructed by integrating 12 Triticeae genomes and three outgroup model genomes to support clade-specific analyses of crops including wheat, barley, and rye.

Scientific Applications:

• Structural Rearrangement Analysis: Macrocollinearity analysis reconstructs structural rearrangements, including two major translocation events involving chromosomes 4A-5A-7B in wheat.
• Evolutionary History Exploration: Collinearity analyses elucidate complex evolutionary histories of specific genes, exemplified by tracing the wheat vernalization gene Vrn2 through translocation, duplication, polyploidization, and gene loss.

Methodology:

Implements a collinearity-incorporating homology inference strategy and a multilevel pipeline integrating macrocollinearity and microscale collinearity, and constructs the Triticeae-GeneTribe database by integrating 12 Triticeae genomes and three outgroup model genomes.